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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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ERROR: Could not find a version that satisfies the requirement actualSonLib (from progressiveCactus==1.0) (from versions: none) #85

Open jenurfor opened 5 years ago

jenurfor commented 5 years ago

Hello,

I was trying to install cactus in the HPC cluster following the instructions but failed for several times. Here are some basic info of my system:

What I have done is shown as followed: pip install virtualenv virtualenv cactus_env source cactus_env/bin/activate git clone https://github.com/ComparativeGenomicsToolkit/cactus.git cd cactus pip install --upgrade toil[all] pip install --upgrade .

Here comes the error messages:

_ERROR: Could not install packages due to an EnvironmentError: [('/data/group/sbs_ssin/applications/cactus/.git/objects/pack/pack-422108fd50e08a06d97ee88fcfa2e34597601922.idx', '/tmp/pip-req-build-1e0dlnns/.git/objects/pack/pack-422108fd50e08a06d97ee88fcfa2e34597601922.idx', "[Errno 13] Permission denied: '/tmp/pip-req-build-1e0dlnns/.git/objects/pack/pack-422108fd50e08a06d97ee88fcfa2e34597601922.idx'"), ('/data/group/sbsssin/applications/cactus/.git/objects/pack/pack-422108fd50e08a06d97ee88fcfa2e34597601922.pack', '/tmp/pip-req-build-1e0dlnns/.git/objects/pack/pack-422108fd50e08a06d97ee88fcfa2e34597601922.pack', "[Errno 13] Permission denied: '/tmp/pip-req-build-1e0dlnns/.git/objects/pack/pack-422108fd50e08a06d97ee88fcfa2e34597601922.pack'")]

And I tried this: pip install --upgrade --user .

This showed up:

ERROR: Can not perform a '--user' install. User site-packages are not visible in this virtualenv.

And I tried this: pip install --upgrade -e .

Resulted this:

_Obtaining file:///data/group/sbs_ssin/applications/cactus Requirement already satisfied, skipping upgrade: decorator in /data/group/sbs_ssin/applications/cactus_env/lib/python3.6/site-packages (from progressiveCactus==1.0) (4.4.0) Collecting subprocess32 (from progressiveCactus==1.0) Using cached https://files.pythonhosted.org/packages/32/c8/564be4d12629b912ea431f1a50eb8b3b9d00f1a0b1ceff17f266be190007/subprocess32-3.5.4.tar.gz Requirement already satisfied, skipping upgrade: psutil in /data/group/sbs_ssin/applications/cactus_env/lib/python3.6/site-packages (from progressiveCactus==1.0) (3.0.1) Requirement already satisfied, skipping upgrade: networkx<3,>=2 in /data/group/sbs_ssin/applications/cactus_env/lib/python3.6/site-packages (from progressiveCactus==1.0) (2.3) Collecting cython (from progressiveCactus==1.0) Using cached https://files.pythonhosted.org/packages/58/2f/b08ad77c639040baafc891621f0cfdb209e2266404ca13c3167970a6f6d6/Cython-0.29.12-cp36-cp36m-manylinux1_x86_64.whl Collecting actualSonLib (from progressiveCactus==1.0) ERROR: Could not find a version that satisfies the requirement actualSonLib (from progressiveCactus==1.0) (from versions: none) ERROR: No matching distribution found for actualSonLib (from progressiveCactus==1.0)_

And I got stuck...

Is there any suggestion please? Your help will be very much appreciated. :-)

jenurfor commented 5 years ago

It seems that the only version available for actualSonLib at the moment is for python2, but the latest version of cactus uses python3...

jenurfor commented 5 years ago

Creating a virtual environment with python2 solved the problem: virtualenv -p /path-to-your-python2/python2.7 name-of-cactus-environment

In my case, it will be like: virtualenv -p /share1/python/2.7.11/bin/python2.7 cactus_env_p2

Then cactus can be installed without this issue while python2 environment being activated.

joelarmstrong commented 5 years ago

Hi,

Sorry about that, didn't see your earlier issue. Cactus only supports Python 2 at the moment. Thanks for the workaround, I will add that to the README in case someone ends up with the same issue of virtualenv being Python 3 by default.